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- EMDB-62269: Structure of hTRPC3 in complex with Nb3-37 at 3.01 angstrom -

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Basic information

Entry
Database: EMDB / ID: EMD-62269
TitleStructure of hTRPC3 in complex with Nb3-37 at 3.01 angstrom
Map data
Sample
  • Complex: TRPC3 tetramer combined with Nb3-37
    • Protein or peptide: Short transient receptor potential channel 3
    • Protein or peptide: Nb3-37
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
KeywordsTRPC3 / DAG / Nb3-37 / nanobody / METAL TRANSPORT
Function / homology
Function and homology information


positive regulation of cardiac muscle hypertrophy in response to stress / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / calcium-activated cation channel activity / cation channel complex / TRP channels / response to ATP ...positive regulation of cardiac muscle hypertrophy in response to stress / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / calcium-activated cation channel activity / cation channel complex / TRP channels / response to ATP / positive regulation of calcium ion transport into cytosol / phototransduction / regulation of cytosolic calcium ion concentration / single fertilization / MECP2 regulates neuronal receptors and channels / response to calcium ion / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Short transient receptor potential channel 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Camelus (mammal)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsChen L / Guo W / Chen Y / Zang J
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303000 China
National Natural Science Foundation of China (NSFC)32225027 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural mechanism of the agonist binding on human TRPC3 channel.
Authors: Yikun Chen / Jiahe Zang / Wenjun Guo / Jiaxuan Xu / Miao Wei / Li Quan / Min Zhu / Xiaole Zhao / Hailin Peng / Yakun Wan / Lei Chen /
Abstract: TRPC3/6/7 channels are cation channels that are directly activated by the second messenger diacylglycerol (DAG). These channels play crucial physiological roles and are implicated in various disease ...TRPC3/6/7 channels are cation channels that are directly activated by the second messenger diacylglycerol (DAG). These channels play crucial physiological roles and are implicated in various disease conditions; however, the binding mechanism of DAG to these channels remains incompletely understood. In this study, we present the structures of human TRPC3 in complex with DAG or synthetic activators, 4n and GSK1702934A. The structural analysis reveals that DAG binds at the L2 site, located near the pore on the extracellular side of TRPC3. Functional assays confirmed that the L2 site serves as the activating site for DAG. Notably, both 4n and GSK1702934A competitively bind to the same site, facilitating channel activation. Moreover, based on the pharmacophore identified from the DAG-bound structure, we found that monoacylglycerols (MAGs) are endogenous activators of TRPC3/6/7 channels, providing new insights into their regulatory mechanisms.
History
DepositionNov 3, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62269.png

Downloads & links

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Map

FileDownload / File: emd_62269.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.51
Minimum - Maximum-2.3905296 - 4.032609
Average (Standard dev.)0.0074534602 (±0.15385038)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.152 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62269_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_62269_additional_1.map
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Half map: #2

Fileemd_62269_half_map_1.map
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Half map: #1

Fileemd_62269_half_map_2.map
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Sample components

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Entire : TRPC3 tetramer combined with Nb3-37

EntireName: TRPC3 tetramer combined with Nb3-37
Components
  • Complex: TRPC3 tetramer combined with Nb3-37
    • Protein or peptide: Short transient receptor potential channel 3
    • Protein or peptide: Nb3-37
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate

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Supramolecule #1: TRPC3 tetramer combined with Nb3-37

SupramoleculeName: TRPC3 tetramer combined with Nb3-37 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Short transient receptor potential channel 3

MacromoleculeName: Short transient receptor potential channel 3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.662812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTKVRKCKE QARVTFPAPE EEEDEGEDEG AEPQRRRRGW RGVNGGLEPR SAPSQREPHG YCPPPFSHGP DLSMEGSPSL RRMTVMREK GRRQAVRGPA FMFNDRGTSL TAEEERFLDA AEYGNIPVVR KMLEESKTLN VNCVDYMGQN ALQLAVGNEH L EVTELLLK ...String:
MSTKVRKCKE QARVTFPAPE EEEDEGEDEG AEPQRRRRGW RGVNGGLEPR SAPSQREPHG YCPPPFSHGP DLSMEGSPSL RRMTVMREK GRRQAVRGPA FMFNDRGTSL TAEEERFLDA AEYGNIPVVR KMLEESKTLN VNCVDYMGQN ALQLAVGNEH L EVTELLLK KENLARIGDA LLLAISKGYV RIVEAILNHP GFAASKRLTL SPCEQELQDD DFYAYDEDGT RFSPDITPII LA AHCQKYE VVHMLLMKGA RIERPHDYFC KCGDCMEKQR HDSFSHSRSR INAYKGLASP AYLSLSSEDP VLTALELSNE LAK LANIEK EFKNDYRKLS MQCKDFVVGV LDLCRDSEEV EAILNGDLES AEPLEVHRHK ASLSRVKLAI KYEVKKFVAH PNCQ QQLLT IWYENLSGLR EQTIAIKCLV VLVVALGLPF LAIGYWIAPC SRLGKILRSP FMKFVAHAAS FIIFLGLLVF NASDR FEGI TTLPNITVTD YPKQIFRVKT TQFTWTEMLI MVWVLGMMWS ECKELWLEGP REYILQLWNV LDFGMLSIFI AAFTAR FLA FLQATKAQQY VDSYVQESDL SEVTLPPEIQ YFTYARDKWL PSDPQIISEG LYAIAVVLSF SRIAYILPAN ESFGPLQ IS LGRTVKDIFK FMVLFIMVFF AFMIGMFILY SYYLGAKVNA AFTTVEESFK TLFWSIFGLS EVTSVVLKYD HKFIENIG Y VLYGIYNVTM VVVLLNMLIA MINSSYQEIE DDSDVEWKFA RSKLWLSYFD DGKTLPPPFS LVPSPKSFVY FIMRIVNFP KCRRRRLQKD IEMGMGNSKS RLNLFTQSNS RVFESHSFNS ILNQPTRYQQ IMKRLIKRYV LKAQVDKEND EVNEGELKEI KQDISSLRY ELLEDKSQAT EELAILIHKL SEKLNPSMLR CE

UniProtKB: Short transient receptor potential channel 3

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Macromolecule #2: Nb3-37

MacromoleculeName: Nb3-37 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Camelus (mammal)
Molecular weightTheoretical: 18.148906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPEFQVQLQE SGGGSVQSGG SLRLSCAASG YTYSRSCLGW FRQAPGKERE RVATIDSDGS TSYADSVKGR FTISQDNAKN TLYLQMNSL KSEDTAMYYC ASKYGSRCQN SLGYMYRGQG TQVTVSSLEI EEQKLISEED LGSGPSRLEE ELRRRLTEHH H HHH

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec...

MacromoleculeName: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
type: ligand / ID: 5 / Number of copies: 4 / Formula: A1L5I
Molecular weightTheoretical: 620.986 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116623
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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